Water quality objectives for body contact recreation (REC-1) in Newport Bay, CA are not being attained. To evaluate the health implications of this non-attainment, a comprehensive health-based investigation was designed and implemented. Bacterial indicator data indicate that exceedances of the water quality objectives are temporally sporadic, geographically limited and most commonly occur during the time of the year and/or in areas of the bay where the REC-1 use is low or non-existent. A disease transmission model produced simulated risk estimates for recreation in the Bay that were below levels considered tolerable by the US EPA (median estimate 0.9 illnesses per 1,000 recreation events). Control measures to reduce pathogen loading to Newport Bay are predicted to reduce risk by an additional 16% to 50%. The results of this study indicate that interpreting the public health implications of fecal indicator data in recreational water may require a more rigorous approach than is currently used.